date:20151112

Re: [Pw_forum] question about small benchmark and pwgui

2015-11-12 Thread Paolo Giannozzi

Replace "nelec=760" with "tot_charge = 2"

P.

On Thu, Nov 12, 2015 at 9:03 PM, mohammed shambakey 
wrote:

> para-speedup.sh
>
> On Thu, Nov 12, 2015 at 9:17 PM, Paolo Giannozzi 
> wrote:
>
>> Which file exactly are you refering to?
>>
>> Paolo
>>
>> On Thu, Nov 12, 2015 at 6:52 PM, mohammed shambakey > > wrote:
>>
>>> Thank you Paolo, but the file still contains "nelec" variable.
>>>
>>> Is it safe to remove it? or something else needs to be changed?
>>>
>>> Regards
>>>
>>> On Thu, Nov 12, 2015 at 10:53 AM, Paolo Giannozzi >> > wrote:
>>>


 On Tue, Nov 10, 2015 at 3:41 PM, mohammed shambakey <
 shambak...@gmail.com> wrote:

>
> 1- I'm trying to run the pwscf-small-benchmark, but it gives me an
> error about namelist. So, I tried to open the generated "large-test.in"
> file in PWgui, but it gives me the following syntax error:
>
> namelist's variable "nelec" not allowed. Skipping the rest of the file
>

 The updated version of the "small" benchmarks is here:

 http://qe-forge.org/gf/download/frsrelease/43/76/pwscf-small-benchmark.tar.gz
 it runs with recent versions of QE, does not contain obsolete variable
 "nelec"

 Paolo
 --
 Paolo Giannozzi, Dept. Chemistry,
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222

 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
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>>>
>>>
>>>
>>> --
>>> Mohammed
>>>
>>> ___
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>>> Pw_forum@pwscf.org
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>>>
>>
>>
>>
>> --
>> Paolo Giannozzi, Dept. Chemistry,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Mohammed
>
> ___
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>



-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] question about small benchmark and pwgui

2015-11-12 Thread mohammed shambakey

para-speedup.sh

On Thu, Nov 12, 2015 at 9:17 PM, Paolo Giannozzi 
wrote:

> Which file exactly are you refering to?
>
> Paolo
>
> On Thu, Nov 12, 2015 at 6:52 PM, mohammed shambakey 
> wrote:
>
>> Thank you Paolo, but the file still contains "nelec" variable.
>>
>> Is it safe to remove it? or something else needs to be changed?
>>
>> Regards
>>
>> On Thu, Nov 12, 2015 at 10:53 AM, Paolo Giannozzi 
>> wrote:
>>
>>>
>>>
>>> On Tue, Nov 10, 2015 at 3:41 PM, mohammed shambakey <
>>> shambak...@gmail.com> wrote:
>>>

 1- I'm trying to run the pwscf-small-benchmark, but it gives me an
 error about namelist. So, I tried to open the generated "large-test.in"
 file in PWgui, but it gives me the following syntax error:

 namelist's variable "nelec" not allowed. Skipping the rest of the file

>>>
>>> The updated version of the "small" benchmarks is here:
>>>
>>> http://qe-forge.org/gf/download/frsrelease/43/76/pwscf-small-benchmark.tar.gz
>>> it runs with recent versions of QE, does not contain obsolete variable
>>> "nelec"
>>>
>>> Paolo
>>> --
>>> Paolo Giannozzi, Dept. Chemistry,
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> Mohammed
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
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Re: [Pw_forum] question about small benchmark and pwgui

2015-11-12 Thread Paolo Giannozzi

Which file exactly are you refering to?

Paolo

On Thu, Nov 12, 2015 at 6:52 PM, mohammed shambakey 
wrote:

> Thank you Paolo, but the file still contains "nelec" variable.
>
> Is it safe to remove it? or something else needs to be changed?
>
> Regards
>
> On Thu, Nov 12, 2015 at 10:53 AM, Paolo Giannozzi 
> wrote:
>
>>
>>
>> On Tue, Nov 10, 2015 at 3:41 PM, mohammed shambakey > > wrote:
>>
>>>
>>> 1- I'm trying to run the pwscf-small-benchmark, but it gives me an error
>>> about namelist. So, I tried to open the generated "large-test.in" file
>>> in PWgui, but it gives me the following syntax error:
>>>
>>> namelist's variable "nelec" not allowed. Skipping the rest of the file
>>>
>>
>> The updated version of the "small" benchmarks is here:
>>
>> http://qe-forge.org/gf/download/frsrelease/43/76/pwscf-small-benchmark.tar.gz
>> it runs with recent versions of QE, does not contain obsolete variable
>> "nelec"
>>
>> Paolo
>> --
>> Paolo Giannozzi, Dept. Chemistry,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Mohammed
>
> ___
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> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] question about small benchmark and pwgui

2015-11-12 Thread mohammed shambakey

Thank you Paolo, but the file still contains "nelec" variable.

Is it safe to remove it? or something else needs to be changed?

Regards

On Thu, Nov 12, 2015 at 10:53 AM, Paolo Giannozzi 
wrote:

>
>
> On Tue, Nov 10, 2015 at 3:41 PM, mohammed shambakey 
> wrote:
>
>>
>> 1- I'm trying to run the pwscf-small-benchmark, but it gives me an error
>> about namelist. So, I tried to open the generated "large-test.in" file
>> in PWgui, but it gives me the following syntax error:
>>
>> namelist's variable "nelec" not allowed. Skipping the rest of the file
>>
>
> The updated version of the "small" benchmarks is here:
>
> http://qe-forge.org/gf/download/frsrelease/43/76/pwscf-small-benchmark.tar.gz
> it runs with recent versions of QE, does not contain obsolete variable
> "nelec"
>
> Paolo
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Mohammed
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[Pw_forum] Quantum Espress 4.0.3 installation issue

2015-11-12 Thread Krishnendu Ghosh

Hello,

I need to use EPW which works with Quantum Espresso 4.0.3. However I am
having issue with installation of that version of QE though the newer
versions work fine. I paste the error messages below. Could someone please
help me fix this?

/usr/include/bits/stdio.h: In function ‘memstat_’:
/usr/include/bits/stdio.h:38: error: nested function ‘vprintf’ declared
‘extern’
/usr/include/bits/stdio.h:37: error: static declaration of ‘vprintf’
follows non-static declaration
/usr/include/bits/stdio.h:46: error: nested function ‘getchar’ declared
‘extern’
/usr/include/bits/stdio.h:45: error: static declaration of ‘getchar’
follows non-static declaration
/usr/include/stdio.h:542: note: previous declaration of ‘getchar’ was here
/usr/include/bits/stdio.h:55: error: nested function ‘fgetc_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:54: error: static declaration of ‘fgetc_unlocked’
follows non-static declaration
/usr/include/stdio.h:565: note: previous declaration of ‘fgetc_unlocked’
was here
/usr/include/bits/stdio.h:65: error: nested function ‘getc_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:64: error: static declaration of ‘getc_unlocked’
follows non-static declaration
/usr/include/stdio.h:554: note: previous declaration of ‘getc_unlocked’ was
here
/usr/include/bits/stdio.h:72: error: nested function ‘getchar_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:71: error: static declaration of
‘getchar_unlocked’ follows non-static declaration
/usr/include/stdio.h:555: note: previous declaration of ‘getchar_unlocked’
was here
/usr/include/bits/stdio.h:81: error: nested function ‘putchar’ declared
‘extern’
/usr/include/bits/stdio.h:80: error: static declaration of ‘putchar’
follows non-static declaration
/usr/include/bits/stdio.h:90: error: nested function ‘fputc_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:89: error: static declaration of ‘fputc_unlocked’
follows non-static declaration
/usr/include/bits/stdio.h:100: error: nested function ‘putc_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:99: error: static declaration of ‘putc_unlocked’
follows non-static declaration
/usr/include/bits/stdio.h:107: error: nested function ‘putchar_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:106: error: static declaration of
‘putchar_unlocked’ follows non-static declaration
/usr/include/bits/stdio.h:127: error: nested function ‘feof_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:126: error: static declaration of ‘feof_unlocked’
follows non-static declaration
/usr/include/stdio.h:831: note: previous declaration of ‘feof_unlocked’ was
here
/usr/include/bits/stdio.h:134: error: nested function ‘ferror_unlocked’
declared ‘extern’
/usr/include/bits/stdio.h:133: error: static declaration of
‘ferror_unlocked’ follows non-static declaration
/usr/include/stdio.h:832: note: previous declaration of ‘ferror_unlocked’
was here
make[1]: *** [memstat.o] Error 1


Thanks,

Krishnendu Ghosh, Graduate Student

University at Buffalo
The State University of New York
Buffalo, NY 14260
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Re: [Pw_forum] GIPAW Problem (Cholesky)

2015-11-12 Thread Davide Ceresoli

Dear Vic,
 could you try disabling the parallel linear algebra by
adding "-ndiag 1" after gipaw.x? also could you try to change
isolve from 0 to 1 or viceversa? third and last possibility:
increase q_gipaw from 0.01 to 0.02 or 0.03.

Best,
 Davide

On 11/11/2015 11:22 PM, Vic Bermudez wrote:
> Hello,
>
>   I'm trying to use GIPAW for the first time and encountering a problem 
> that
> isn't discussed at the users' forum. I'm using GIPAW vers. v.5.0.2 (svn rev.
> 9392), and I get this error message soon after execution starts:
>
> 
>   Error in routine  cdiaghg (2785):
>problems computing cholesky
>   
>   stopping ...
>
>   Here's my GIPAW input file:
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Re: [Pw_forum] Problems with high ecutwfc for a C H As F S containing compound

2015-11-12 Thread Paolo Giannozzi

BHS (Bachelet-Hamann-Schlueter) may be hard, but the two, S and As, that
appear in the list, aren't. H and C are also not especially hard. Flourine
is by far the hardest, because 1) 2p states of F are notoriously hard, and
2) HGH (Hartwigsen-Goedecker-Hutter) pseudopotentials are typically hard.
Anyway: interesting physical quantities typically converge much better than
absolut energies.


Paolo

On Thu, Nov 12, 2015 at 11:03 AM, Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear Stephan
> If I remember well, the BHS pseudopotentials used to be very hard, even if
> at 320 Ry you might almost converge all-electron calculations! However, in
> my opinion, you might try with a small system (e.g., CH4, AsH3 or SF6 with
> your PPs) to see when the TDDFT or GW results obtained with yambo do not
> change anymore with the ecutwfc cutoff. It could turn out that your
> convergence criterion is too tight, and that stable eigenvalues (they
> usually
> converge faster than total energy), are enough in your case.
> HTH
> Giuseppe
>
> On Thursday, November 12, 2015 10:19:17 AM Ludwig, Stephan wrote:
> > Hi,
> >
> > I have the problem that I want to simulate an organic conductor.
> >
> > I'm looking for convergence of the total energy with respect to the
> ecutwfc.
> >
> > In the end I want to do optical investigations with the yambo program.
> >
> > As a criterion for convergence I decided to choose a total energy
> difference of less than one meV per atom between two scf calculations.
> >
> >
> >
> >
> > ecutwfc   tot energy (Ry) tot energy per atom (Ry)tot energy
> per Atom in eV
> > 80-3173,1197  -13,4454224576  -182,9342903348
> > 90-3178,8757  -13,4698122881  -183,2661308812
> > 100   -3183,225   -13,4882415254  -183,5168734262
> > 120   -3189,049   -13,5129194915  -183,852634257
> > 140   -3192,482   -13,5274661017  -184,0505509693
> > 160   -3194,507   -13,5360466102  -184,1672947335
> > 180   -3195,727   -13,5412161017  -184,2376292482
> > 200   -3196,459   -13,5443177966  -184,279829957
> > 220   -3197,176   -13,5473559322  -184,3211658972
> > 240   -3197,176   -13,5473559322  -184,3211658972
> > 260   -3197,34-13,5480508475  -184,3306207008
> > 280   -3197,446   -13,5485-184,3367317324
> > 300   -3197,501   -13,5487330508  -184,3399025507
> > 320   -3197,5499  -13,5489402542  -184,3427216964
> >
> >
> > As you see I can't reach the convergence criterion.
> >
> > As I understood the ecutwfc which is suitable depends on the used
> pseudopotentials.
> >
> > I used these ones from the QE-database:
> >
> >
> >
> > H 1.00790 H.pz-vbc.UPF
> >  C 12.01100 C.pz-vbc.UPF
> >  F 18.98800 F.pz-hgh.UPF
> >  S 32.06500 S.pz-bhs.UPF
> >  As 74.92200 As.pz-bhs.UPF
> >
> >
> >
> > Does anybody knows which one causes the necessity of such a high ecutwfc?
> >
> > Can anybody supply or suggest more suitable pseudos?
> >
> >
> >
> > Thanks and regards
> >
> >
> >
> > Stephan
> >
> >
> >
> > The input file I use looks like this:
> >
> >
> >
> > 
> >  title = 'etot_vs_ecutwfc' ,
> >  calculation = 'scf' ,
> >  max_seconds = 5.D+5,
> >  restart_mode = 'from_scratch',
> >  wf_collect = .TRUE.,
> >  outdir = './' ,
> >  wfcdir = './' ,
> >  pseudo_dir = '/home/st/st_st/st_phy72394/pseudo/' ,
> >  prefix = 'MeDH-TTPetot_vs_ecutwfc' ,
> >  /
> >  
> >  ibrav = -12,
> >  A = 32.783 ,
> >  B = 7.995 ,
> >  C = 11.170 ,
> >  cosAB = 0 ,
> >  cosAC = -0.132602381688 ,
> >  cosBC = 0 ,
> >  nat = 236,
> >  ntyp = 5,
> >  ecutwfc = 280 ,
> >  occupations = 'smearing' ,
> >  degauss = 0.02 ,
> >  force_symmorphic = .TRUE.,
> >  smearing = 'gaussian' ,
> >  exxdiv_treatment = 'gygi-baldereschi' ,
> >  /
> >  
> >  conv_thr = 1.0D-8
> >  /
> > ATOMIC_SPECIES
> >  H 1.00790 H.pz-vbc.UPF
> >  C 12.01100 C.pz-vbc.UPF
> >  F 18.98800 F.pz-hgh.UPF
> >  S 32.06500 S.pz-bhs.UPF
> >  As 74.92200 As.pz-bhs.UPF
> > ATOMIC_POSITIONS angstroms
> >  S 5.52835 0.29521 2.16999
> >  S 21.91985 4.29246 2.16999
> >  S 4.78777 7.69929 7.70567
> >  S 21.17927 3.70204 7.70567
> >  S 8.91117 6.37745 3.91040
> >  S 25.30267 2.38020 3.91040
> >  S 8.17058 1.61705 9.44608
> >  S 24.56208 5.61430 9.44608
> >  S 8.53628 0.30838 1.68728
> >  S 24.92778 4.30563 1.68728
> >  S 7.79569 7.68612 7.22296
> >  S 24.18719 3.68887 7.22296
> >  S 5.91488 6.35256 4.41083
> >  S 22.30638 2.35531 4.41083
> >  S 5.17429 1.64194 9.94651
> >  S 21.56579 5.63919 9.94651
> > As 31.25307 7.42312 4.40640
> > As 14.86156 3.42587 4.40640
> > As 30.51248 0.57138 9.94208
> > As 14.12098 4.56863 9.94208
> >  S 22.77175 0.24544 7.42335
> >  S 6.38025 4.24269 7.42335
> >  S 23.51233 7.74906 1.88767
> >  S 7.12083 3.75181 1.88767
> >  S 22.41272 6.31548 5.17143
> >  S 6.02122 2.31823 5.17143
> >  S 21.67213 1.67902 10.70711
> >  S 5.28063 5.67627 10.70711
> >  S 19.75130 0.27959 7.86510
> >  S 3.35980 4.27684 7.86510
> >  S 20.49188 7.71491 2.32941
> >  S 4.10038 3.71766 2.32941
> >  S 19.39879

Re: [Pw_forum] Problems with high ecutwfc for a C H As F S containing compound

2015-11-12 Thread Giuseppe Mattioli


Dear Stephan
If I remember well, the BHS pseudopotentials used to be very hard, even if at 
320 Ry you might almost converge all-electron calculations! However, in 
my opinion, you might try with a small system (e.g., CH4, AsH3 or SF6 with your 
PPs) to see when the TDDFT or GW results obtained with yambo do not 
change anymore with the ecutwfc cutoff. It could turn out that your convergence 
criterion is too tight, and that stable eigenvalues (they usually 
converge faster than total energy), are enough in your case.
HTH
Giuseppe

On Thursday, November 12, 2015 10:19:17 AM Ludwig, Stephan wrote:
> Hi,
> 
> I have the problem that I want to simulate an organic conductor.
> 
> I'm looking for convergence of the total energy with respect to the ecutwfc.
> 
> In the end I want to do optical investigations with the yambo program.
> 
> As a criterion for convergence I decided to choose a total energy difference 
> of less than one meV per atom between two scf calculations.
> 
> 
> 
>  
> ecutwfc   tot energy (Ry) tot energy per atom (Ry)tot energy per 
> Atom in eV   
> 80-3173,1197  -13,4454224576  -182,9342903348 
> 90-3178,8757  -13,4698122881  -183,2661308812 
> 100   -3183,225   -13,4882415254  -183,5168734262 
> 120   -3189,049   -13,5129194915  -183,852634257  
> 140   -3192,482   -13,5274661017  -184,0505509693 
> 160   -3194,507   -13,5360466102  -184,1672947335 
> 180   -3195,727   -13,5412161017  -184,2376292482 
> 200   -3196,459   -13,5443177966  -184,279829957  
> 220   -3197,176   -13,5473559322  -184,3211658972 
> 240   -3197,176   -13,5473559322  -184,3211658972 
> 260   -3197,34-13,5480508475  -184,3306207008 
> 280   -3197,446   -13,5485-184,3367317324 
> 300   -3197,501   -13,5487330508  -184,3399025507 
> 320   -3197,5499  -13,5489402542  -184,3427216964 
> 
> 
> As you see I can't reach the convergence criterion.
> 
> As I understood the ecutwfc which is suitable depends on the used 
> pseudopotentials.
> 
> I used these ones from the QE-database:
> 
> 
> 
> H 1.00790 H.pz-vbc.UPF 
>  C 12.01100 C.pz-vbc.UPF 
>  F 18.98800 F.pz-hgh.UPF 
>  S 32.06500 S.pz-bhs.UPF 
>  As 74.92200 As.pz-bhs.UPF 
> 
> 
> 
> Does anybody knows which one causes the necessity of such a high ecutwfc?
> 
> Can anybody supply or suggest more suitable pseudos?
> 
> 
> 
> Thanks and regards
> 
> 
> 
> Stephan
> 
> 
> 
> The input file I use looks like this:
> 
> 
> 
> 
>  title = 'etot_vs_ecutwfc' ,
>  calculation = 'scf' ,
>  max_seconds = 5.D+5,
>  restart_mode = 'from_scratch',
>  wf_collect = .TRUE.,
>  outdir = './' ,
>  wfcdir = './' ,
>  pseudo_dir = '/home/st/st_st/st_phy72394/pseudo/' ,
>  prefix = 'MeDH-TTPetot_vs_ecutwfc' ,
>  /
>  
>  ibrav = -12,
>  A = 32.783 ,
>  B = 7.995 ,
>  C = 11.170 ,
>  cosAB = 0 ,
>  cosAC = -0.132602381688 ,
>  cosBC = 0 ,
>  nat = 236,
>  ntyp = 5,
>  ecutwfc = 280 ,
>  occupations = 'smearing' ,
>  degauss = 0.02 ,
>  force_symmorphic = .TRUE.,
>  smearing = 'gaussian' ,
>  exxdiv_treatment = 'gygi-baldereschi' ,
>  /
>  
>  conv_thr = 1.0D-8
>  /
> ATOMIC_SPECIES
>  H 1.00790 H.pz-vbc.UPF 
>  C 12.01100 C.pz-vbc.UPF 
>  F 18.98800 F.pz-hgh.UPF 
>  S 32.06500 S.pz-bhs.UPF 
>  As 74.92200 As.pz-bhs.UPF 
> ATOMIC_POSITIONS angstroms 
>  S 5.52835 0.29521 2.16999
>  S 21.91985 4.29246 2.16999
>  S 4.78777 7.69929 7.70567
>  S 21.17927 3.70204 7.70567
>  S 8.91117 6.37745 3.91040
>  S 25.30267 2.38020 3.91040
>  S 8.17058 1.61705 9.44608
>  S 24.56208 5.61430 9.44608
>  S 8.53628 0.30838 1.68728
>  S 24.92778 4.30563 1.68728
>  S 7.79569 7.68612 7.22296
>  S 24.18719 3.68887 7.22296
>  S 5.91488 6.35256 4.41083
>  S 22.30638 2.35531 4.41083
>  S 5.17429 1.64194 9.94651
>  S 21.56579 5.63919 9.94651
> As 31.25307 7.42312 4.40640
> As 14.86156 3.42587 4.40640
> As 30.51248 0.57138 9.94208
> As 14.12098 4.56863 9.94208
>  S 22.77175 0.24544 7.42335
>  S 6.38025 4.24269 7.42335
>  S 23.51233 7.74906 1.88767
>  S 7.12083 3.75181 1.88767
>  S 22.41272 6.31548 5.17143
>  S 6.02122 2.31823 5.17143
>  S 21.67213 1.67902 10.70711
>  S 5.28063 5.67627 10.70711
>  S 19.75130 0.27959 7.86510
>  S 3.35980 4.27684 7.86510
>  S 20.49188 7.71491 2.32941
>  S 4.10038 3.71766 2.32941
>  S 19.39879 6.33792 5.62425
>  S 3.00729 2.34067 5.62425
>  S 20.13937 1.65658 0.08857
>  S 3.74787 5.65383 0.08857
>  S 25.96310 0.08881 6.99046
>  S 9.57160 4.08606 6.99046
>  S 26.70368 7.90569 1.45478
>  S 10.31218 3.90844 1.45478
>  S 25.56056 6.28376 4.68983
>  S 9.16906 2.28651 4.68983
>  S 24.81997 1.71074 10.22551
>  S 8.42848 5.70799 10.22551
>  S 12.08748 6.57702 3.54505
>  S 28.47898 2.57977 3.54505
>  S 11.34689 1.41748 9.08073
>  S 27.73839 5.41473 9.08073
>  S 11.74373 0.68898 1.53781
>  S 28.13523 4.68623 1.53781
>  S 11.00315 7.30552 7.07349
>  S 27.39465 3.30827 7.07349
>  C 2.50124 7.97352 2.72134
>  C 18.89274 3.97627 2.72134
>  C 1.76066 0.02098 8.25702
>  C 18.15215 4.01823 8.25702
>  H 2.98979 0.63970

[Pw_forum] Problems with high ecutwfc for a C H As F S containing compound

2015-11-12 Thread Ludwig , Stephan

Hi,

I have the problem that I want to simulate an organic conductor.

I'm looking for convergence of the total energy with respect to the ecutwfc.

In the end I want to do optical investigations with the yambo program.

As a criterion for convergence I decided to choose a total energy difference of 
less than one meV per atom between two scf calculations.



 
ecutwfc tot energy (Ry) tot energy per atom (Ry)tot energy per Atom in 
eV   
80  -3173,1197  -13,4454224576  -182,9342903348 
90  -3178,8757  -13,4698122881  -183,2661308812 
100 -3183,225   -13,4882415254  -183,5168734262 
120 -3189,049   -13,5129194915  -183,852634257  
140 -3192,482   -13,5274661017  -184,0505509693 
160 -3194,507   -13,5360466102  -184,1672947335 
180 -3195,727   -13,5412161017  -184,2376292482 
200 -3196,459   -13,5443177966  -184,279829957  
220 -3197,176   -13,5473559322  -184,3211658972 
240 -3197,176   -13,5473559322  -184,3211658972 
260 -3197,34-13,5480508475  -184,3306207008 
280 -3197,446   -13,5485-184,3367317324 
300 -3197,501   -13,5487330508  -184,3399025507 
320 -3197,5499  -13,5489402542  -184,3427216964 


As you see I can't reach the convergence criterion.

As I understood the ecutwfc which is suitable depends on the used 
pseudopotentials.

I used these ones from the QE-database:



H 1.00790 H.pz-vbc.UPF 
 C 12.01100 C.pz-vbc.UPF 
 F 18.98800 F.pz-hgh.UPF 
 S 32.06500 S.pz-bhs.UPF 
 As 74.92200 As.pz-bhs.UPF 



Does anybody knows which one causes the necessity of such a high ecutwfc?

Can anybody supply or suggest more suitable pseudos?



Thanks and regards



Stephan



The input file I use looks like this:




 title = 'etot_vs_ecutwfc' ,
 calculation = 'scf' ,
 max_seconds = 5.D+5,
 restart_mode = 'from_scratch',
 wf_collect = .TRUE.,
 outdir = './' ,
 wfcdir = './' ,
 pseudo_dir = '/home/st/st_st/st_phy72394/pseudo/' ,
 prefix = 'MeDH-TTPetot_vs_ecutwfc' ,
 /
 
 ibrav = -12,
 A = 32.783 ,
 B = 7.995 ,
 C = 11.170 ,
 cosAB = 0 ,
 cosAC = -0.132602381688 ,
 cosBC = 0 ,
 nat = 236,
 ntyp = 5,
 ecutwfc = 280 ,
 occupations = 'smearing' ,
 degauss = 0.02 ,
 force_symmorphic = .TRUE.,
 smearing = 'gaussian' ,
 exxdiv_treatment = 'gygi-baldereschi' ,
 /
 
 conv_thr = 1.0D-8
 /
ATOMIC_SPECIES
 H 1.00790 H.pz-vbc.UPF 
 C 12.01100 C.pz-vbc.UPF 
 F 18.98800 F.pz-hgh.UPF 
 S 32.06500 S.pz-bhs.UPF 
 As 74.92200 As.pz-bhs.UPF 
ATOMIC_POSITIONS angstroms 
 S 5.52835 0.29521 2.16999
 S 21.91985 4.29246 2.16999
 S 4.78777 7.69929 7.70567
 S 21.17927 3.70204 7.70567
 S 8.91117 6.37745 3.91040
 S 25.30267 2.38020 3.91040
 S 8.17058 1.61705 9.44608
 S 24.56208 5.61430 9.44608
 S 8.53628 0.30838 1.68728
 S 24.92778 4.30563 1.68728
 S 7.79569 7.68612 7.22296
 S 24.18719 3.68887 7.22296
 S 5.91488 6.35256 4.41083
 S 22.30638 2.35531 4.41083
 S 5.17429 1.64194 9.94651
 S 21.56579 5.63919 9.94651
As 31.25307 7.42312 4.40640
As 14.86156 3.42587 4.40640
As 30.51248 0.57138 9.94208
As 14.12098 4.56863 9.94208
 S 22.77175 0.24544 7.42335
 S 6.38025 4.24269 7.42335
 S 23.51233 7.74906 1.88767
 S 7.12083 3.75181 1.88767
 S 22.41272 6.31548 5.17143
 S 6.02122 2.31823 5.17143
 S 21.67213 1.67902 10.70711
 S 5.28063 5.67627 10.70711
 S 19.75130 0.27959 7.86510
 S 3.35980 4.27684 7.86510
 S 20.49188 7.71491 2.32941
 S 4.10038 3.71766 2.32941
 S 19.39879 6.33792 5.62425
 S 3.00729 2.34067 5.62425
 S 20.13937 1.65658 0.08857
 S 3.74787 5.65383 0.08857
 S 25.96310 0.08881 6.99046
 S 9.57160 4.08606 6.99046
 S 26.70368 7.90569 1.45478
 S 10.31218 3.90844 1.45478
 S 25.56056 6.28376 4.68983
 S 9.16906 2.28651 4.68983
 S 24.81997 1.71074 10.22551
 S 8.42848 5.70799 10.22551
 S 12.08748 6.57702 3.54505
 S 28.47898 2.57977 3.54505
 S 11.34689 1.41748 9.08073
 S 27.73839 5.41473 9.08073
 S 11.74373 0.68898 1.53781
 S 28.13523 4.68623 1.53781
 S 11.00315 7.30552 7.07349
 S 27.39465 3.30827 7.07349
 C 2.50124 7.97352 2.72134
 C 18.89274 3.97627 2.72134
 C 1.76066 0.02098 8.25702
 C 18.15215 4.01823 8.25702
 H 2.98979 0.63970 2.22534
 H 19.38129 4.63695 2.22534
 H 2.24920 7.35480 7.76102
 H 18.64071 3.35755 7.76102
 H 1.85588 0.41427 3.28266
 H 18.24738 4.41152 3.28266
 H 1.11530 7.58023 8.81834
 H 17.50680 3.58298 8.81834
 H 2.05231 7.38359 2.11352
 H 18.44381 3.38634 2.11352
 H 1.31173 0.61091 7.64920
 H 17.70323 4.60816 7.64920
 F 32.09159 6.20228 3.55280
 F 15.70009 2.20503 3.55280
 F 31.35101 1.79222 9.08848
 F 14.95951 5.78947 9.08848
 F 31.99917 0.61481 3.45094
 F 15.60767 4.61206 3.45094
 F 31.25859 7.37969 8.98662
 F 14.86709 3.38244 8.98662
 F 30.39326 0.65482 5.22458
 F 14.00176 4.65207 5.22458
 F 29.65268 7.33968 10.76026
 F 13.26118 3.34243 10.76026
 F 30.47339 6.23106 5.35854
 F 14.08189 2.23381 5.35854
 F 29.73280 1.76344 10.89422
 F 13.34130 5.76069 10.89422
 F 29.96030 7.30601 3.28598
 F 13.56880 3.30876 3.28598
 F 29.21972 0.68849 8.82166
 F 12.82821 4.68574 8.82166
 F -0.26088 7.52461 5.52461
 F

Re: [Pw_forum] troubles in using epsilon.x on spin-polarized pwscf calculations (Paolo Giannozzi)

2015-11-12 Thread Paolo Giannozzi

On Tue, Nov 10, 2015 at 9:30 AM, Roberto Gaspari 
wrote:

>
> I have installed qe 5.2.1 on my internal cluster using gnu compilers as
> well as on cineca, by copying and pasting the lines in the file
> README.CINECA_fermi in the install directory of the qe distribution from
> module purge to make all.
> In both cases I get the same behavior as described in the previous email.
> A friend of mine, with qe installed using intel compilers, could complete
> the
> simulation, so could that perhaps be a compiler issue?
>

unlikely, because compiler issues are compiler-dependent and seldom appear
on two different compilers. It might related to how the code is run, but it
is hard to find what happens and why without a precise description of what
is done and how (and sometimes, especially if it is a sizable calculation,
even WITH a precise description)

Paolo

-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] question about small benchmark and pwgui

2015-11-12 Thread Paolo Giannozzi

On Tue, Nov 10, 2015 at 3:41 PM, mohammed shambakey 
wrote:

>
> 1- I'm trying to run the pwscf-small-benchmark, but it gives me an error
> about namelist. So, I tried to open the generated "large-test.in" file in
> PWgui, but it gives me the following syntax error:
>
> namelist's variable "nelec" not allowed. Skipping the rest of the file
>

The updated version of the "small" benchmarks is here:
http://qe-forge.org/gf/download/frsrelease/43/76/pwscf-small-benchmark.tar.gz
it runs with recent versions of QE, does not contain obsolete variable
"nelec"

Paolo
-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] 5.2.1 release building issue

2015-11-12 Thread Paolo Giannozzi

On Tue, Nov 10, 2015 at 12:21 PM, Éric Germaneau 
wrote:

> xild -static-intel  -openmp -o iotk_print_kinds.x iotk_print_kinds.o
> libiotk.a
> ipo: warning #11016: Warning unknown option -static-intel
> xild: executing 'ld'
>
>

> I'm wondering if someone else also got this error.
>

I haven't,  but clearly that the problem is that "xild" (whatever it is)
doesn't like the option "-static-intel". Try to remove it from make.sys

Paolo

-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] HSE Screening Parameter

2015-11-12 Thread Paolo Giannozzi

With a 24x24x24 grid and a huge 120 Ry cutoff the code likely goes out of
memory (it needs a bunch of wavefunctions in real space)  and stops before
starting to compute the exact exchange contribution, so what you get is
just the initial scf loop with PBE. There are examples in PW/tests for HSE
(hse-si???.in) that you can easily modify and quickly run, showing that HSE
results do actually depend upon the value of screening_parameter. Your
input stops immediately because stresses are not implemented with hybrid
functionals (forces are, AFAIK).

On Fri, Nov 6, 2015 at 3:31 PM, Ref Fymz  wrote:

> Yes I did, it just prints out the corresponding kpoint points and
> occupation numbers. No added data about forces / stresses / individual
> energy contributions are contained. As I said, when I use an 8x8x8 grid
> this works fine, but with a 24x24x24 it doesn't.
>
> On 5 November 2015 at 09:02, Ref Fymz  wrote:
>
>> Dear pw_forum,
>>
>>
>> I am trying to use the HSE hybrid functional within quantum espresso, I
>> have an 8 atom cubic silicon cell, and I have converged my k-point grid,
>> q-point grid, and my wavefunction ecut. However, regardless of how much I
>> change my screening parameter (from 0.0 bohr^-1 all the way to 100
>> bohr^-1), the difference between my lowest unoccupied and highest occupied
>> state remains about 0.61 eV, this points towards a problem. Can anybody
>> point me in the right direction?
>>
>> Also, when I do an scf run, I'm not getting the pressures / forces
>> printed in the file, despite asking for them, is this due to the density of
>> my k-point and q-point grid?
>>
>> The only other thing I can think it could be from is the ecutvcut /
>> x_gamma_extrapolation / exxdiv_treatment. Has anybody else used QE for
>> silicon successfully?
>>
>> My input looks like this;
>>
>>  
>> prefix='silicon',
>> pseudo_dir = 'espresso/pseudo/',
>> outdir='./tmp'
>> tprnfor = .true.
>> tstress = .true.
>> restart_mode = 'from_scratch'
>>
>>  /
>>  
>> ibrav = 1, celldm(1) =10.327, nat= 8, ntyp= 1,
>> ecutwfc = 120, input_dft = 'hse'
>> nqx1 = 8, nqx2 = 8, nqx3 = 8
>> nbnd = 32
>> screening_parameter = 100
>> occupations = 'fixed'
>>  /
>>  
>> diagonalization='cg'
>> conv_thr = 1.0e-9
>>  /
>> ATOMIC_SPECIES
>>  Si 28.086 Si.pbe-mt_fhi.UPF
>>
>> ATOMIC_POSITIONS alat
>>  Si 0.0   0.0  0.0
>>  Si 0.5   0.5  0.0
>>  Si 0.5   0.0  0.5
>>  Si 0.0   0.5  0.5
>>  Si 0.25 0.25 0.25
>>  Si 0.75 0.75 0.25
>>  Si 0.75 0.25 0.75
>>  Si 0.25 0.75 0.75
>>
>> K_POINTS automatic
>> 24 24 24 0 0 0
>>
>>
>>
>> Thanks,
>>
>>
>> Phil
>>
>
>
> ___
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>



-- 
Paolo Giannozzi, Dept. Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] question about small benchmark and pwgui

Re: [Pw_forum] question about small benchmark and pwgui

Re: [Pw_forum] question about small benchmark and pwgui

Re: [Pw_forum] question about small benchmark and pwgui

[Pw_forum] Quantum Espress 4.0.3 installation issue

Re: [Pw_forum] GIPAW Problem (Cholesky)

Re: [Pw_forum] Problems with high ecutwfc for a C H As F S containing compound

Re: [Pw_forum] Problems with high ecutwfc for a C H As F S containing compound

[Pw_forum] Problems with high ecutwfc for a C H As F S containing compound

Re: [Pw_forum] troubles in using epsilon.x on spin-polarized pwscf calculations (Paolo Giannozzi)

Re: [Pw_forum] question about small benchmark and pwgui

Re: [Pw_forum] 5.2.1 release building issue

Re: [Pw_forum] HSE Screening Parameter

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